This repository contains some proteomics data from:

A. The results from a multi-omics study of silicosis mouse model (DOI: 10.1038/s41392-022-00959-3). The proteomics data was analysis by MaxQuant, and the gene counts data for RNA-seq was generated using HISAT2 and the R package GenomicsAlignments.

B. A benchmark proteomics dataset obtained by spiking Yeast and E. coli proteome into a Hela background. The proteomics data was measured using an Orbitrap Fusion Lumos Tribrid mass spectrometer, either in Data Dependent Acquisition (DDA) or Data Independent Acquisition (DIA) mode. The DDA data was analyzed using either MaxQuant or FragPipe, while the DIA data was analyzed using Spectronaut or DIA-NN without library. The reference proteome used includes reviewed sequences of Homo sapiens, S.cerevisiae, and Escherichia coli (strain K12) downloaded from Uniprot.

All quantitative tables are compressed into .gz files.